schrodinger.application.desmond.packages.parch module

This program edits a given trajectory as follows:
  1. Align each frame to a reference structure as specified via the -ref-mae option. If this option is not specified, the one from the input CMS file will be used as the reference structure. The atoms to align can be specified via the -align-asl option. If it is not specified, the program will select the atoms automatically based on the following precedences from high to low: A. For protein or covalent-ligand FEP systems, the backbone of the mutated

    residues will be selected for alignment.

    1. If protein is present in the system, all backbone atoms will be selected for alignment.
    2. If it is a FEP system for the solvent leg, the core atoms will be selected for alignment.

    D. All solute atoms will be selected for alignment. Note that the value of -align-asl will be applied to both the reference structure and each trajectory frame. If you wish to use a different atom selection for the reference structure only, you can specify that via the -ref-asl option. In any cases, the atoms selected in both the reference structure and each trajectory frame should match each other. If selected atoms include protein backbone atoms, all non-backbone atoms will be ignored.

  2. For each frame, remove the solvent molecules beyond the region of interest, which is herein referred to as the ‘dew point’ and can be specified via the -dew-asl option. The number of solvent molecules to retain can be specified via the -n option.

  3. In the case of FEP system, atoms corresponding to the other end point will also be removed.

The default number of solvent molecules retained by this script is 200. This is approximately the number of water molecules in a spherical droplet of radius 11.5 Angstroms at the temperature of 300 K. To estimate the number of water molecules to retain, use this table:

nWat: 50 100 200 300 400 500 600 700 800 900 1000 r(A): 7.2 9.1 11.5 13.0 14.3 15.4 16.4 17.3 18.0 18.8 19.6
schrodinger.application.desmond.packages.parch.generate_reduced_fep_trajectory(cms_fname, trj_fname, out_basename, dew_asl, lambda_val, ref_ct_fname=None, nsolvent=200)

Utility function to generate a ‘reduced’ fep trajectory, where the ligands are solvated by nsolvent water molecules and the system is aligned on the first frame.

Parameters:
  • cms_fname – filename of the cms file
  • trj_fname – filename of the trajectory
  • out_basename – the basename of output cms/trj
  • dew_asl – asl of the ligand around which the waters will be kept
  • lambda_val – lambda endpont – 0 or 1
  • ref_ct_fname – Structure file containing reference coordinates
  • nsolvent – number of solvent molecules to retain
Returns:

a list of generated files/directories

Return type:

list of str or an empty list

schrodinger.application.desmond.packages.parch.main(argv=None)